ClinVar Miner

Submissions for variant NM_001184880.2(PCDH19):c.3262G>A (p.Ala1088Thr)

gnomAD frequency: 0.00009  dbSNP: rs370078729
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000766557 SCV000241953 likely benign not provided 2019-11-18 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000188341 SCV000614418 uncertain significance not specified 2017-04-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001065355 SCV001230311 uncertain significance Developmental and epileptic encephalopathy, 9 2024-12-09 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1088 of the PCDH19 protein (p.Ala1088Thr). This variant is present in population databases (rs370078729, gnomAD 0.009%). This missense change has been observed in individual(s) with clinical features of developmental and epileptic encephalopathy (internal data). ClinVar contains an entry for this variant (Variation ID: 206306). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt PCDH19 protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002514024 SCV003586270 likely benign Inborn genetic diseases 2022-08-08 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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